Biology subjects

Miyazaki, T.

Publications and source records attributed to Miyazaki, T..

13 recordsLinked to original sources

bioRxiv2025

Kidney-specific lipid metabolism underlies stable chemical individuality in domestic cats and other felids

Domestic cats uniquely accumulate lipid droplets (LDs) in renal proximal tubular epithelial cells, but their chemical composition and biological functions remain unknown. Here, we identify a distinctive renal specialization in felids: lipid droplets enriched in branched-chain fatty acids (BFAs). These BFAs accumulate as triglyceride components and are excreted in urine as free fatty acids with stable and individually distinctive profiles. Behavioral assays show that cats discriminate urine samples based on BFA composition, even against complex volatile backgrounds, suggesting BFAs as robust, metabolically encoded olfactory signatures for individual recognition. Comparative analyses of non-domesticated felids reveal that BFA production is broadly conserved but exhibits both species-specific and individual variation. These findings demonstrate how a core metabolic pathway has been evolutionarily co-opted into a chemical signature system. This discovery highlights an unusual integration of renal physiology with social communication and expand our understanding of lipid metabolism, organ-level adaptation, and the evolution of chemical individuality in mammals. Significance statementUnique lipid droplets in felid kidneys reveal how organ-specific metabolism can be adapted for social communication.

zoology↗

bioRxiv2025

Insulin-like androgenic gland factor regulates the development of internal and external secondary sexual characteristics in juvenile male kuruma prawn Marsupenaeus japonicus

In decapod crustaceans, insulin-like androgenic gland factor (IAG) is a well-known peptide hormone produced by the androgenic gland, a male-specific endocrine organ. In certain species classified within Pleocyemata, experimental manipulation of IAG signaling has successfully altered both internal and external sexual characteristics, leading to sex reversal. Therefore, IAG is considered a key regulator of male sexual differentiation and maturation and is thought to be a crustacean androgen. In the kuruma prawn Marsupenaeus japonicus (Dendrobranchiata), an important fishery species in Japan, a homologous molecule known as Maj-IAG has been identified. However, its physiological function in males remains poorly understood. In this context, we conducted Maj-IAG knockdown (KD) via RNA interference in juvenile male M. japonicus. Over a 9-week period, Maj-IAG KD significantly inhibited the development of the petasma, male-specific external copulatory structure, and parts of the internal reproductive organs, such as the vas deferens and seminal vesicles. In contrast, somatic growth and testicular development were unaffected by Maj-IAG KD. Histological analysis of the testes revealed no evident abnormalities such as degeneration of testicular structures or abnormal arrest of germ cell differentiation. These findings indicate that Maj-IAG partially governs the development of male secondary sexual characteristics in juveniles and further suggest that once testicular differentiation is initiated, the maintenance and development of the testis proceeds without dependence on Maj-IAG. Our study provides fundamental insights that may contribute to the advancement of functional sex reversal technologies in penaeid shrimps. HighlightsO_LILong-term gene knockdown of the insulin-like androgenic gland factor gene (Maj-IAG) was successfully achieved in Marsupenaeus japonicus. C_LIO_LISomatic growth and spermatogenesis were not affected by Maj-IAG knockdown. C_LIO_LIMaj-IAG is involved in the development of male secondary sexual characteristics in juvenile prawns, including the external male copulatory structures and certain parts of the internal male reproductive organs. C_LI

zoology↗

bioRxiv2025

De novo chemo-optogenetics through rational small-molecule design and TRAP display

Optical control of biomolecules is a powerful technique for biological research, but current tools derived from natural proteins face significant limitations. Engineering these proteins to meet researchers needs remains challenging. In this study, we present a novel approach to the de novo creation of tailored chemo-optogenetic tools. This method combines the rational design of synthetic photo-switchable molecules with in vitro selection of artificial protein binders that specifically recognize a particular conformation of these molecules. We demonstrate the utility of this approach by generating artificial proteins that bind exclusively to the cis-form of designed azobenzene derivatives. The newly created pairs enable sustained protein activation with a single light pulse and allow for precise, reversible, and repeatable switching of cellular processes using two distinct wavelengths of light in mammalian cells. This de novo technique provides tailored synthetic photoswitch-protein binder pairs, expanding the potential for optical biomolecule manipulation.

synthetic biology↗

bioRxiv2024

Self-organized acoustic behavior in bats arises from simple rules

Although self-organized behavior has been extensively studied in the movement of group-behaving animals, such as fish or birds, far less attention has been paid to vocal behavior in animal groups, especially in mammals. Here, by testing the vocal response of echolocating bats (Miniopterus fuliginosus) to the playback of jamming stimuli in the lab, we discovered a mathematical model that can well describe vocal frequency control by bats in response to jamming stimuli mimicking echolocation sounds emitted in a group of bats. We then extended the model to a group of flying bats and observed frequency-adjusting behavior by which the frequency differences for the group increased overall, similar to a previous observation on group-flying bats. Further, we showed the frequency-adjusting behavior led to less potential misdetections by echolocation in a group. Our findings suggest this frequency-adjusting behavior is a self-organized vocal behavior that mitigates conflicts within a group, one achieved via simple behavioral rules, as in other types of collective animal behavior.

animal behavior and cognition↗

bioRxiv2024

Stratification of viral shedding patterns in saliva of COVID-19 patients

Living with COVID-19 requires continued vigilance against the spread and emergence of variants of concern (VOCs). Rapid and accurate saliva diagnostic testing, alongside basic public health responses, is a viable option contributing to effective transmission control. Nevertheless, our knowledge regarding the dynamics of SARS-CoV-2 infection in saliva is not as advanced as our understanding of the respiratory tract. Here we analyzed longitudinal viral load data of SARS-CoV-2 in saliva samples from 144 patients with mild COVID-19 (a combination of our collected data and published data). Using a mathematical model, we quantified individual-level viral dynamics and stratified them into three groups using a clustering approach. Notably, the three groups exhibited distinct differences viral RNA detection durations: 11.5 days (95% CI: 10.6 to 12.4), 17.4 days (16.6 to 18.2), and 30.0 days (28.1 to 31.8), respectively. Surprisingly, this stratified grouping remained unexplained despite our analysis of 47 types of clinical data, including basic demographic information, clinical symptoms, results of blood tests, and vital signs. Additionally, we quantified the expression levels of 92 micro-RNAs in a subset of saliva samples, but these also failed to explain the observed stratification, although the mir-1846 level may have been weakly correlated with peak viral load. Our study provides insights into SARS-CoV-2 infection dynamics in saliva, highlighting the challenges in predicting the duration of viral RNA detection without indicators that directly reflect an individuals immune response, such as antibody induction. Given the significant individual heterogeneity in the kinetics of saliva viral shedding, identifying biomarker(s) for viral shedding patterns will be crucial for improving public health interventions in the era of living with COVID-19.

microbiology↗

bioRxiv2024

Lignin isolated by microwave-assisted acid-catalyzed solvolysis induced cell death on mammalian tumor cells by modulating apoptotic pathways

Lignin, the most abundant renewable aromatic polymer, has been shown to suppress the growth of mammalian tumor cells. Despite being a textbook example, there is little information on the biological activity of lignin in relation to its molecular structure or the molecular mechanisms by which lignin suppresses tumor cells in mammalian species. Here, we prepared Microwave-assisted Acid-catalyzed Solvolysis Lignin (MASL) and assessed its effects on human and mouse tumor cells. Our data showed MASL significantly reduced viability of tumor cells by modulating apoptotic pathways. MASL treatment upregulated TNF-, Fas, and FasL expression levels, while suppressing anti-apoptotic NF-{kappa}B and mTOR pathways in tumor cells. In-vivo experiments were also performed using tumor-bearing mice to confirm the anti-tumor effects of MASL. An administration of MASL significantly suppressed tumor growth in mice in association with elevation of caspase 3 expression. These findings strongly suggest the potential usefulness of low molecular weight lignin as an effective therapeutic against malignancies.

cancer biology↗

bioRxiv2023

ORP9-PH domain-based fluorescent reporters for visualizing phosphatidylinositol 4-phosphate dynamics in living cells

Fluorescent reporters that visualize phosphatidylinositol 4-phosphate (PI4P) in living cells are indispensable to elucidate the roles of this fundamental lipid in cell physiology. However, currently available PI4P reporters have limitations, such as Golgi-biased localization and low detection sensitivity. Here, we present a series of fluorescent PI4P reporters based on the pleckstrin homology (PH) domain of oxysterol-binding protein-related protein 9 (ORP9). We show that the green fluorescent protein AcGFP1-tagged ORP9-PH domain can be used as a fluorescent PI4P reporter to detect cellular PI4P across its wide distribution at multiple cellular locations, including the plasma membrane (PM), Golgi, endosomes, and lysosomes with high specificity and contrast. We also developed blue, red, and near-infrared fluorescent PI4P reporters suitable for multicolor fluorescence imaging experiments. Finally, we demonstrate the utility of the ORP9-PH domain-based reporter to visualize dynamic changes in the PI4P distribution and level in living cells upon synthetic ER-PM membrane contact manipulation and GPCR stimulation. This work offers a new set of genetically encoded fluorescent PI4P reporters that are practically useful for the study of PI4P biology.

cell biology↗

bioRxiv2023

Microbiome ssRNA as an environmental cue to activate TLR13-dependent tissue-protective programs in CD5Lhi hepatic macrophages

Hepatic macrophages maintain liver homeostasis, but little is known about the signals that activate the hepatoprotective programs within macrophages. Here, we show that toll-like receptor 13 (TLR13), a sensor of bacterial 23S ribosomal RNA (rRNA), senses microbiome RNAs to drive tissue-protective responses in CD5Lhi hepatic macrophages. Splenomegaly and hepatomegaly developed in the absence of the endosomal RNase, RNaseT2, via TLR13-dependent macrophage proliferation. Furthermore, TLR13 in hepatic Ly6Clo macrophages activated the transcription factors LXR and MafB, leading to expression of tissue-clearance molecules, such as CD5L, C1qb, and Axl. Consequently, Rnaset2-/- mice developed resistance to acute liver injury caused by challenges with acetaminophen and lipopolysaccharide + D-galactosamine. TLR13 responses in Rnaset2-/- mice were impaired by antibiotics, suggesting that TLR13 were activated by microbiome rRNAs, which was detected in the sera and hepatic macrophages. Repeated administration of wild-type mice with the TLR13 ligand, rather than other TLR ligands, selectively increased the number of Kupffer cells, which expressed immunoregulatory and tissue-clearance genes as hepatic macrophages in Rnaset2-/- mice did. Our results suggest that microbiome ssRNA serves as an environmental cue for initiating tissue-protective TLR13 responses in hepatic macrophages. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/540294v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@69614eorg.highwire.dtl.DTLVardef@737c69org.highwire.dtl.DTLVardef@1ecd9eforg.highwire.dtl.DTLVardef@d7e10d_HPS_FORMAT_FIGEXP M_FIG In the absence of an endosomal RNase, RNase T2, microbiome RNAs circulating in the vasculature activate TLR13 in hepatic macrophages to drive hepatoprotective responses through expression of immunoregulatory and tissue-clearance molecules. Consequently, mice lacking RNase T2 are resistant against acute liver injuries caused by acetaminophen and LPS + D-galactosamine. C_FIG

immunology↗

bioRxiv2022

Deep learning for histopathological subtyping and grading of lung adenocarcinoma

The histopathological distinction of lung adenocarcinoma (LADC) subtypes is subject to high inter-observer variability, which can compromise the optimal assessment of the patient prognosis. Therefore, this study developed convolutional neural networks (CNNs) capable of distinguishing LADC subtypes and predicting disease-specific survival, according to the LADC tumour grades established recently by the International Association for the Study of Lung Cancer pathology committee. Consensus LADC ground truth histopathological images were obtained from seventeen expert pulmonary pathologists and one pathologist in training. Two deep learning models (AI-1 and AI-2) were trained with EfficientNet b3 architecture to predict eight different LADC classes (lepidic, acinar, papillary, micropapillary, solid, invasive mucinous adenocarcinoma, other carcinoma types, and no carcinoma cells). Furthermore, the trained models were tested on an independent cohort of 133 patients. The models achieved high precision, recall, and F1-scores exceeding 0.90 for most of the LADC classes. Clear stratification of the three LADC grades was reached in predicting the disease-specific survival by the two models. Moreover, the grading prediction of one of the trained models was more accurate than those of 14 out of 15 pulmonary pathologists involved in the study (p=0.0003). Both trained models showed high stability in the segmentation of each pair of predicted grades with low variation in the hazard ratio across 200 bootstrapped samples. These findings indicate that the trained CNNs improve the diagnostic accuracy of the pathologist, standardise LADC subtype recognition, and refine LADC grade assessment. Thus, the trained models are promising tools that may assist in the routine evaluation of LADC subtypes and grades in clinical practice.

pathology↗

bioRxiv2021

An intramolecular scrambling path controlled by a gatekeeper in Xkr8 phospholipid scramblase

Xkr8-Basigin is a phospholipid scramblase at plasma membranes that is activated by kinase or caspase. We investigated its structure at a resolution of 3.8[A]. Its membrane-spanning region had a cuboid-like structure stabilized by salt bridges between hydrophilic residues in helices in the lipid layer. The molecule carried phosphatidylcholine in a cleft on the surface that may function as an entry site for phospholipids. Five charged residues placed from top to bottom inside the molecule were essential for providing a path for scrambling phospholipids. A tryptophan residue was present at the extracellular end of the pathway and its mutation made the Xkr8-Basigin complex constitutively active, indicating its function as a gatekeeper. The structure of Xkr8-Basigin provides novel insights into the molecular mechanisms underlying phospholipid scrambling.

biochemistry↗

bioRxiv2019

Periosteum-derived Osteocrin regulates bone growth through both endochondral ossification and intramembranous ossification

During development of long bones, two mechanistically distinct processes contribute to long- and short-axis growth. Endochondral ossification in the growth plate leads to the long-axis growth, while intramembranous ossification including apposition in the periosteum regulates the short axis growth. Here, we show that periosteal osteoblast-derived secretory peptide, Osteocrin (OSTN), promotes both types of long bone growth through potentiation of signaling by C-type natriuretic peptide (CNP), because OSTN inhibits the clearance of CNP by binding to natriuretic peptide receptor 3 (NPR3). The mice lacking OSTN showed less bone mass in trabecular and cortical regions than the control mice, suggesting the dual functions of OSTN in long bone growth. We found that OSTN regulated trabecular bone formation by inducing proliferation and maturation of chondrocytes possibly through enhancing CNP-dependent signaling. Besides the contribution of OSTN to long axis growth, we demonstrated that OSTN together with CNP induced osteoblast differentiation of periosteum-derived multipotent progenitor cells expressing NPR3. These data suggest that OSTN induces long bone growth through endochondral ossification and osteoblast specification of multipotent progenitor cells in the periosteum.

developmental biology↗

bioRxiv2019

GABA neurons in the ventral tegmental area regulate non-rapid eye movement sleep in mice

The daily sleep/wakefulness cycle is regulated by coordinated interactions between sleep- and wakefulness-regulating neural circuitry. However, the detailed neural circuitry mediating sleep is far from understood. Here, we found that glutamic acid decarboxylase 67 (Gad67)-positive GABAergic neurons in the ventral tegmental area (VTAGad67+) are a key regulator of non-rapid eye movement (NREM) sleep in mice. VTAGad67+ neurons project to multiple brain areas implicated in sleep/wakefulness regulation such as the lateral hypothalamus (LH) and dorsal raphe nucleus. Chemogenetic activation of VTAGad67+ neurons promoted NREM sleep with higher delta power whereas optogenetic inhibition of these neurons induced prompt arousal from NREM sleep under highly somnolescent conditions, but not during REM sleep. In vivo fiber photometry recordings revealed that VTAGad67+ neurons showed the highest population activity in NREM sleep and the lowest activity in REM sleep. Acute brain slice electrophysiology combined with optogenetics revealed that VTAGad67+ neurons directly innervate and inhibit wake-promoting orexin/hypocretin neurons in the LH by releasing GABA. Taken together, we reveal that VTAGad67+ neurons play a crucial role in the regulation of NREM sleep.

neuroscience↗

bioRxiv2017

Hippo signaling restricts cells in the second heart field that differentiate into Islet-1-positive atrial cardiomyocytes

AbstractCardiac precursor cells (CPCs) in the first heart field (FHF) and the second heart field (SHF) present at both arterial and venous poles assemble to form a cardiac tube in zebrafish. Hippo kinase cascade is essential for proper heart formation; however, it remains elusive how Hippo signal contributes to early cardiac fate determination. We here demonstrate that mutants of large tumor suppressor kinase 1/2 (lats1/2) exhibited an increase in a SHF marker, Islet1 (Isl1)-positive and hand2 promoter-activated venous pole atrial cardiomyocytes (CMs) and that those showed expansion of the domain between between the anterior and the posterior lateral plate mesoderm. Consistently, TEAD-8 dependent transcription was activated in caudal region of the left ALPM cells that gave rise to the venous pole atrial CMs. Yap1/Wwtr1-promoted bmp2b expression was essential for Smad-regulated hand2 expression in the left ALPM, indicating that Hippo signaling restricts the SHF cells originating from the left ALPM that move toward the venous pole.

developmental biology↗